Variant Normalization¶

How gbcms prepares variants before counting — validation, left-alignment, and homopolymer decomposition.

Overview¶

Before counting any reads, every variant passes through the preparation pipeline in prepare_variants(). This ensures consistent, biologically correct coordinates regardless of how the input was generated.

flowchart LR
    Input(["📄 Input Variant"]):::start --> S1["Step 1: MAF Anchor"]
    S1 --> S2["Step 2: REF Validation"]
    S2 -->|"REF_MISMATCH"| Fail(["❌ Rejected"]):::fail
    S2 -->|"PASS*"| S3["Step 3: Left-Alignment"]
    S3 --> S4["Step 4: ref_context Fetch"]
    S4 --> S5["Step 5: Homopolymer Detection"]
    S5 --> Output(["✅ PreparedVariant"]):::pass

    classDef start fill:#9b59b6,color:#fff,stroke:#7d3c98,stroke-width:2px;
    classDef step fill:#3498db,color:#fff,stroke:#2471a3,stroke-width:2px;
    classDef fail fill:#e74c3c,color:#fff,stroke:#c0392b,stroke-width:2px;
    classDef pass fill:#27ae60,color:#fff,stroke:#1e8449,stroke-width:2px;
    class S1,S2,S3,S4,S5 step;

Each input variant produces exactly one PreparedVariant, even if validation fails — this guarantees output row count always matches input.

Step 1: MAF Anchor Resolution¶

MAF files represent indels using - dashes. gbcms converts them to VCF-style anchor-based coordinates, which requires fetching the anchor base from the reference FASTA.

Step 2: REF Validation¶

The REF allele is compared against the reference genome at the stated position. An exact match passes immediately. If the exact match fails, a similarity score is computed — variants with ≥90% base match are corrected to the FASTA REF and proceed to counting.

flowchart TD
    Fetch["Fetch ref bases at pos"] --> Exact{"Exact match?"}
    Exact -->|"Yes"| Pass(["✅ PASS"]):::pass
    Exact -->|"No"| Sim["Compute similarity\n(matching bases / max length)"]
    Sim --> Thresh{"≥ 90%?"}
    Thresh -->|"Yes"| Corrected(["⚠️ PASS + WARN_REF_CORRECTED\nFASTA REF used downstream"]):::warn
    Thresh -->|"No"| Fail(["❌ FAIL + REF_MISMATCH\n→ excluded from counting"]):::fail

    classDef pass fill:#27ae60,color:#fff,stroke:#1e8449,stroke-width:2px;
    classDef warn fill:#f39c12,color:#fff,stroke:#d68910,stroke-width:2px;
    classDef fail fill:#e74c3c,color:#fff,stroke:#c0392b,stroke-width:2px;

When a variant gets a WARN_REF_CORRECTED reason (verdict stays PASS), the MAF's REF allele is replaced with the FASTA sequence for all downstream steps (left-alignment, haplotype construction). The original MAF REF is preserved in original_ref for auditing.

Step 3: Left-Alignment¶

For indels and complex variants, gbcms applies bcftools-style left-alignment to ensure consistent positioning in repetitive regions.

After alignment, the variant type is re-detected based on the new allele lengths:

Step 4: ref_context Fetch (Adaptive)¶

For indels and complex variants, a flanking reference sequence is fetched around the (possibly normalized) position. This context serves two purposes:

1. Windowed indel detection — Safeguard 3 uses ref_context to verify that shifted indels delete/insert the expected reference bases
2. Phase 3 alignment — the context is used to build REF and ALT haplotypes for dual-haplotype alignment (WFA triage → PairHMM). See Phase 3: Alignment Fallback.

Adaptive Context Padding¶

By default, gbcms dynamically adjusts the context padding based on nearby tandem repeats. This prevents ambiguous SW alignments in repetitive regions where a fixed padding might consist entirely of the repeat motif.

Multi-Anchor Footprint Sweep¶

Historically, scanning only the variant's strict anchor base caused miscalculations for left-aligned INDELs, as the trailing INDEL mutations generated by BWA mapping often fell outside the default 5bp padding window.

The engine now performs a Multi-Anchor Footprint Sweep. It scans across the entire variant footprint (pos through pos + ref_len) looking for tandem repeats, and extracts the maximum necessary padding to clear the repeat entirely.

flowchart LR
    SweepFootprint["Sweep variant footprint\n(pos → pos + ref_len)"] --> RepFound{"Tandem repeat\nfound?"}
    RepFound -->|"Yes (span = S)"| Formula["padding = max(5, S/2 + 3)\ncapped at 50bp"]
    RepFound -->|"No"| Default["padding = 5bp (default)"]
    Formula --> Fetch["Fetch ref_context"]
    Default --> Fetch

Example: Poly-A Insertion¶

Variant: chr7:100 A→AAAAAAAAAAAAA (12bp poly-A insertion)
Footprint: chr7:100-101
Flanking: ...AAAAAAAAAA[anchor]AAAAAAAAAA...

Sweep Detected: homopolymer max span=20bp → padding = max(5, 20/2+3) = 13bp

Fixed padding=5:     AAAAA + REF/ALT + AAAAA  (all A's — ambiguous, BWA alignments drop)
Adaptive padding=13: GCTTAAAAA... + REF/ALT + ...AAAAATTGAC  (anchored)

Supported Repeat Types¶

Step 5: Homopolymer Decomposition Detection¶

Some variant callers merge nearby events (e.g., a 1bp deletion + SNV in a homopolymer) into a single complex variant with an inflated deletion size. For example, CCCCCC→T when the reads actually show CCCCCC→CCCCT (a D(1) + C→T).

Detection Criteria¶

All four conditions must be met:

flowchart LR
    C1{"C1: REF is homopolymer?\n(all same base, ≥3bp)"}
    C2{"C2: Net deletion?\n(ref_len > alt_len)"}
    C3{"C3: ALT last base ==\nnext ref base after span?"}
    C4{"C4: ALT last base ≠\nhomopolymer base?"}
    Detected(["🔍 Decomposition detected"]):::detect
    Skip(["⏭️ Skip — not a decomposition"]):::skip

    C1 -->|Yes| C2
    C2 -->|Yes| C3
    C3 -->|Yes| C4
    C4 -->|Yes| Detected

    C1 -->|No| Skip
    C2 -->|No| Skip
    C3 -->|No| Skip
    C4 -->|No| Skip

    classDef detect fill:#f39c12,color:#fff,stroke:#d68910,stroke-width:2px;
    classDef skip fill:#95a5a6,color:#fff,stroke:#7f8c8d,stroke-width:2px;

Corrected Allele Construction¶

When detected, a corrected ALT allele is built by keeping most of the homopolymer intact and appending the SNV base:

Example:  REF = CCCCCC, ALT = T, next_ref_base = T

Step 1: homopolymer base = C
Step 2: Confirmed: alt_last (T) == next_ref_base (T), T ≠ C
Step 3: corrected_alt = C × (ref_len - 1) + alt_last = CCCCC + T = CCCCT

Dual-Counting Flow¶

The corrected variant is stored in PreparedVariant.decomposed_variant. During counting, both the original and corrected alleles are counted independently. The result with the higher alt_count wins:

flowchart TD
    Input(["⚡ Decomposition detected"]):::warn
    Input -->|"in parallel"| CountOrig
    Input -->|"in parallel"| CountDecomp

    CountOrig["count_bam(original: CCCCCC→T)"]
    CountDecomp["count_bam(corrected: CCCCCC→CCCCT)"]

    CountOrig --> Compare
    CountDecomp --> Compare
    Compare{"corrected AD > original AD?"}

    Compare -->|"Yes"| UseDecomp["Return corrected counts"] --> FlagWarn["reason +=\nWARN_HOMOPOLYMER_DECOMP"]:::warn
    Compare -->|"No"| UseOrig["Return original counts"] --> FlagPass["gbcms_status = PASS"]:::pass

    classDef warn fill:#f39c12,color:#fff,stroke:#d68910,stroke-width:2px;
    classDef pass fill:#27ae60,color:#fff,stroke:#1e8449,stroke-width:2px;

Validation Status Reference¶

Status is carried in two fields: a verdict, gbcms_status (exactly PASS or FAIL), and a |-separated reason list, gbcms_status_reason (empty for a clean PASS). Both appear in the MAF (two columns) and the VCF INFO (GS = verdict, GSR = reasons). | is used (never ;/,, which are VCF-unsafe), so the reason string is byte-identical in the MAF and the VCF.

Reasons stack: a PASS variant can carry WARN_REF_CORRECTED|WARN_HOMOPOLYMER_DECOMP.

Limitations¶

1. Left-alignment only — gbcms left-aligns but does not right-align. If your input is right-aligned, the windowed scan (±5bp) may still catch it, but left-alignment is recommended.
2. Dynamic normalization window — Starting at 100bp, the window automatically doubles (up to 2500bp) when a variant shifts to the window edge. In practice, this covers even variants in centromeric/telomeric repeats. Variants shifted beyond 2500bp won't be corrected.
3. Homopolymer detection is conservative — only triggers for homopolymer REF ≥3bp with a clear D(n)+SNV pattern. Other miscollapsed events are not detected.

Related¶

• gbcms normalize — CLI command for standalone normalization
• Input Formats — VCF/MAF coordinate conventions
• Allele Classification — How reads are classified after normalization